Unipept

POST /api/v1/pept2prot
Returns the set of UniProt entries containing a given tryptic peptide.

This method returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab when performing a search with the Tryptic Peptide Analysis in the web interface.

Request

The pept2prot method can be used by doing a HTTP POST-request (preferred) or GET-request to http://api.unipept.ugent.be/api/v1/pept2prot. Parameters can be included in the request body (POST) or in the query string (GET). The only required parameter is input[], which takes one or more tryptic peptides.

input

input[] is a required parameter that takes one or more tryptic peptides. Unipept will return the list of UniProt entries that contain any of the input[] peptides in their protein sequence. To pass multiple peptides at once, simply add multiple input[] parameters (see example).

Input size

Unipept puts no restrictions on the number of peptides passed to the input[] parameter. Keep in mind that searching for lots of peptides at once may cause the request to timeout or, in the case of a GET-request, exceed the maximum URL length. When performing bulk searches, we suggest splitting the input set over requests of 100 peptides each.

equate_il

equate_il is an optional parameter and can either be true or false. When not set explicitly, the parameter defaults to false. When the parameter is set to true, isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt entries. This setting is similar to checking the Equate I and L? checkbox when performing a search with the Tryptic Peptide Analysis in the web interface.

extra

extra is an optional parameter and can either be true or false. When not set explicitly, the parameter defaults to false. When the parameter is set to true, Unipept will return additional information fields. See the response section for an overview of the information fields returned.

Performance penalty

Setting extra to true has a performance penalty inferred from additional database queries. Do not use this parameter unless the extra information fields are needed.

Response

Matching UniProt entries are returned as a list of JSON objects. By default, each object contains the following information fields extracted from the UniProt entry:

  • peptide: the peptide that matched this record
  • uniprot_id: the UniProt accession number of the matching record
  • New protein_name: the name of the protein of the matching record
  • taxon_id: the NCBI taxon id of the organism associated with the matching record

When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt entry:

  • taxon_name: the name of the organism associated with the matching UniProt entry
  • ec_references: a space separated list of associated EC numbers
  • go_references: a space separated list of associated GO terms
  • refseq_ids: a space separated list of associated RefSeq accession numbers
  • refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
  • insdc_ids: a space separated list of associated insdc accession numbers
  • insdc_protein_ids: a space separated list of associated insdc protein accession numbers

Parameters

Name Description
input[]
required

Tryptic peptide to search for. Add multiple parameters to search for multiple peptides.

Value: String
equate_il
optional

Equate isoleucine (I) and leucine (L).

Value: Must be true or false (default)
extra
optional

Return additional information fields if true.

Value: Must be true or false (default)

Examples

Example Retrieve all UniProt entries containing a given tryptic peptide

This example retrieves all UniProt entries containing the peptide AIPQLEVARPADAYETAEAYR. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.

POST 
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2prot \
-d 'input[]=AIPQLEVARPADAYETAEAYR'
GET 
http://api.unipept.ugent.be/api/v1/pept2prot.json?input[]=AIPQLEVARPADAYETAEAYR

Response

[
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    uniprot_id: 'A7A5N6',
    protein_name: 'Transketolase',
    taxon_id: 411481
  },
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    uniprot_id: 'A1A1M7',
    protein_name: 'Transketolase',
    taxon_id: 367928
  }
]

Example Retrieve all UniProt entries containing any of multiple tryptic peptides

This example retrieves all UniProt entries containing either the tryptic peptide AIPQLEVARPADAYETAEAYR or the tryptic peptide APVLSDSSCK. The result is the same as the combination of this search and this search with the Tryptic Peptide Analysis in the web interface.

POST 
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2prot \
-d 'input[]=AIPQLEVARPADAYETAEAYR' \
-d 'input[]=APVLSDSSCK'
GET 
http://api.unipept.ugent.be/api/v1/pept2prot.json?input[]=AIPQLEVARPADAYETAEAYR&input[]=APVLSDSSCK

Response

[
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    uniprot_id: 'A7A5N6',
    protein_name: 'Transketolase',
    taxon_id: 411481
  },
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    uniprot_id: 'A1A1M7',
    protein_name: 'Transketolase',
    taxon_id: 367928
  },
  {
    peptide: 'APVLSDSSCK',
    uniprot_id: 'P00761',
    protein_name: 'Trypsin',
    taxon_id: 9823
  },
  {
    peptide: 'APVLSDSSCK',
    uniprot_id: 'C5IWV5',
    protein_name: 'Trypsinogen',
    taxon_id: 9823
  },
  {
    peptide: 'APVLSDSSCK',
    uniprot_id: 'F1SRS2',
    protein_name: 'Uncharacterized protein',
    taxon_id: 9823
  }
]

Example Retrieve all UniProt entries containing a single tryptic peptide, while equating I and L

This example retrieves all UniProt entries containing the tryptic peptide APVISDSSCK. In searching, isoleucine (I) and leucine (L) are considered equal. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.

POST 
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2prot \
-d 'input[]=APVISDSSCK' \
-d 'equate_il=true'
GET 
http://api.unipept.ugent.be/api/v1/pept2prot.json?input[]=APVISDSSCK&equate_il=true

Response

[
  {
    peptide: 'APVISDSSCK',
    uniprot_id: 'P00761',
    protein_name: 'Trypsin',
    taxon_id: 9823
  },
  {
    peptide: 'APVISDSSCK',
    uniprot_id: 'C5IWV5',
    protein_name: 'Trypsinogen',
    taxon_id: 9823
  },
  {
    peptide: 'APVISDSSCK',
    uniprot_id: 'F1SRS2',
    protein_name: 'Uncharacterized protein',
    taxon_id: 9823
  }
]

Example Retrieve all UniProt entries containing a single tryptic peptide and return extra information

This example retrieves all UniProt entries containing the tryptic peptide AIPQLEVARPADAYETAEAYR, including additional information fields that are not returned by default. The result is the same as this search with the Tryptic Peptide Analysis in the web interface.

POST 
$ curl -X POST -H 'Accept: application/json' api.unipept.ugent.be/api/v1/pept2prot \
-d 'input[]=AIPQLEVARPADAYETAEAYR' \
-d 'extra=true'
GET 
http://api.unipept.ugent.be/api/v1/pept2prot.json?input[]=AIPQLEVARPADAYETAEAYR&extra=true

Response

[
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    uniprot_id: 'A7A5N6',
    protein_name: 'Transketolase',
    taxon_id: 411481,
    taxon_name: 'Bifidobacterium adolescentis L2-32',
    ec_references: '2.2.1.1',
    go_references: '',
    refseq_ids: '',
    refseq_protein_ids: '',
    insdc_ids: 'AAXD02000028',
    insdc_protein_ids: 'EDN82874.1'
  },
  {
    peptide: 'AIPQLEVARPADAYETAEAYR',
    uniprot_id: 'A1A1M7',
    protein_name: 'Transketolase',
    taxon_id: 367928,
    taxon_name: 'Bifidobacterium adolescentis ATCC 15703',
    ec_references: '',
    go_references: '',
    refseq_ids: 'NC_008618.1',
    refseq_protein_ids: 'YP_909692.1',
    insdc_ids: 'AP009256',
    insdc_protein_ids: 'BAF39610.1'
  }
]

Try it

Use the API explorer form below to call the pept2prot method on live data and see the response.

Request


Response

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